Utopia's first incarnation was in 2002 as Utopia Tools, which was downloaded a modest 200 times each month. McDermott has more ambitious plans for Utopia Documents.

Utopia's research associate Philip McDermott

• What's your pitch?"Modern science produces masses of data, but scientists usually only get to publish articles about the highlights, and once they are published articles are frozen in time. So a lot of important knowledge gets lost or hidden.

"Utopia Documents links scientific research papers to the data and to the community. It enables publishers to enhance their publications with additional material, interactive graphs and models. It allow the reader to access a wealth of data resources directly from the paper they are viewing, makes private notes and start public conversations. It does all this on normal PDFs, and never alters the original file. We are targeting the PDF, since they still have around 80% readership over online viewing.

"Semantics, loose-coupling, fingerprinting and linked-data are the key ingredients. All the data is described using ontologies, and a plug-in system allows third parties to integrate their database or tool within a few lines of script. We use fingerprinting to allow us to recognise what paper a user is reading, and to spot duplicates. All annotations are held remotely, so that wherever you view a paper, the result is the same."

• How do you make money?"Our viewing software is free, and it's free to make public comments. Larger customers will want to annotate and discuss documents in private: we're able to provide bespoke back-end solutions so they can have complete control over their data."

• How are you surviving the downturn?"As a research group, we're a not-for-profit setup, so we just need to bring in enough money to cover our costs. Even that is quite tricky though, and set to get harder as the cuts to the UK research budget bite. That said, we're getting a growing amount of interest from industry, so we're fairly optimistic about the future."

• What's your background?"I'm originally a software engineer from the mobile devices world, before I returned to academia to do my doctorate. Since then I've been researching the application of modern data management techniques to scientific data. Our research group has a history of virtual reality and scientific data visualisation."

• What makes your business unique?"We sit somewhere between academia and the business world. Our passion is research, but practical research that can actually be used by real working scientists."

• What has been your biggest achievement so far?"At last year's Portland Press launch , David Thorne selected the word 'cleavage' accidentally in the demo paper; Utopia Documents dutifully brought back only images and descriptions of 'cleaved proteins'... much to our relief."

• Who in the tech business inspires you?" Clay Shirky . He's very insightful and has a pragmatic attitude I admire. I like the approach of the 37Signals guys too, although we've actually chosen Python over Ruby for our scripting language. Sorry, guys."

• What's your biggest challenge?"Funding. Since we fall between two worlds, we have to convince businesses to invest in academia and research councils to invest in an application, both of which can be difficult."

• What's the most important web tool that you use each day? "I'm an OmniFocus convert, it leaves your mind free to do other things."

• Name your closest competitors"Some applications allow you to annotate a PDF, but they change the underlying file which is no good for what we want. Mendeley are in a nearby ballpark, although they appear more focused on the scientific articles themselves, whereas we are more interested in their actual content."

• Where do you want the company to be in five years?"The default reader for scientific articles."

• Sell to Google, or be bigger than Google?"We'd like to choose the middle way: license to Google!"